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PubMed2004

Internet continuing education for health care professionals: an integrative review.

INTRODUCTION: The objective was to review key articles and research studies on practices, preferences, and evaluation of on-line continuing education used by health care professionals. METHODS: Data sources included searches of the MEDLINE, CINAHL, and ERIC databases (January 1990 to June 2004) and manual searches of the Journal of Continuing Education in the Health Professions and the Journal of Continuing Education in Nursing. Articles included reviews and research studies focusing on the use of Internet CE by health care professionals. The articles were categorized according to intervention, subjects, study design, and key findings. RESULTS: Seventeen articles were eligible and were reviewed. Although in-person CE remains the most frequent and most preferred format, Internet CE is gaining in popularity. Most participants who engage in on-line CE are satisfied with the experience and find it to be an effective learning format. Barriers to on-line CE include technical difficulties and lack of computer knowledge. DISCUSSION: Although the Internet is an effective and satisfactory educational format, barriers to use of the Internet for CE still exist. Additional studies are needed to measure the impact of Internet CE on practice performance, reduce barriers to on-line CE, and identify appropriate theoretical frameworks for on-line learning.

Canada↗
PubMed2002

Framework stability of nanoporous inorganic structures upon template extraction and calcination: a theoretical study of gallophosphate polymorphs.

A systematic computational study of gallophosphates was undertaken. First, lattice energy minimization calculations using a formal-charge shell model potential have been carried out on a series of hypothetical gallium phosphates derived from their metallogallophosphate, aluminophosphate, or aluminosilicate analogues through atomic substitution. The minimized structures show the typical features in terms of bond angles and distances as expected in zeolitic gallophosphates. Second, the crystal structures of several gallophosphates in their calcined forms have been predicted, using for each compound lattice energy minimization and an initial model derived from its as-synthesized templated form. All the modified structures thus have the same GaPO(4) composition. The lattice energies of all the simulated gallophosphate structures were compared to that of GaPO(4)-quartz as a reference structure. Interestingly, among all predicted calcined structures, various zeolitic topologies were found. The study of the energetics of these zeotypic structures showed a linear dependence of lattice energy upon density. Strikingly, a few simulated structures showed unrealistic structural features, such as important framework distortions, often associated with the occurrence of a hexameric unit in the original as-synthesized structures. Also, those gallophosphates with structural faults were found in the upper part of the energy/density plot. To address the validity of our force field calculations in these special cases, first principles calculations were undertaken on ULM-4, chosen as a typical representative structure. Indeed, the qualitative agreement found between our results and those obtained with the nonlocal density functional theory demonstrates the robustness of our force field. Further minimization also showed that the inclusion of polarizability is crucial for yielding results comparable with those obtained using first principles methods.

Journal Article↗
PubMed2000

Computational models of the basal ganglia.

Computer simulation studies and mathematical analysis of models of the basal ganglia are being used increasingly to explore theories of basal ganglia function. We review the implications of these new models for a general understanding of basal ganglia function in normal as well as in diseased brains. The focus is on their functional similarities rather than on the details of mathematical methodologies and simulation techniques. Most of the models suggest a vital role for the basal ganglia in learning. Although this interest in learning is partly driven by experimental results associating the acute firing of dopamine cells with reward prediction in monkeys, some of the models have preceded the electrophysiological results. Another common theme of the models is selection. In this case, the striatum is seen as detecting and selecting cortical contexts for access to basal ganglia output. Although the behavioral consequences of this selection are hard to define, the models provide frameworks within which to explore these ideas empirically. This provides a means of refining our understanding of basal ganglia function and to consider dysfunction within the new logical frameworks.

Animals↗
PubMed1994

Detection of bilateral symmetry using spatial filters.

When bilaterally symmetric images are spatially filtered and thresholded, a subset of the resultant 'blobs' cluster around the axis of symmetry. Consequently, a quantitative measure of blob alignment can be used to code the degree of symmetry and to locate the axis of symmetry. Four alternative models were tested to examine which components of this scheme might be involved in human detection of symmetry. Two used a blob-alignment measure, operating on the output of either isotropic or oriented filters. The other two used similar filtering schemes, but measured symmetry by calculating the correlation of one half of the pattern with a reflection of the other. Simulations compared the effect of spatial jitter, proportion of matched to unmatched dots and width or location of embedded symmetrical regions, on models' detection of symmetry. Only the performance of the oriented filter + blob-alignment model was consistent with human performance in all conditions. It is concluded that the degree of feature co-alignment in the output of oriented filters is the cue used by human vision to perform these tasks. The broader computational role that feature alignment detection could play in early vision is discussed, particularly for object detection and image segmentation. In this framework, symmetry is a consequence of a more general-purpose grouping scheme.

Computer Simulation↗
PubMed1994

Generalized dual-energy-window scatter compensation in spatially varying media for SPECT.

The detection of scattered photons in the photopeak energy window hinders accurate activity estimation in single-photon-emission computed tomography (SPECT). To compensate for photons scattered in spatially varying media, a framework for generalized dual-energy-window scatter subtraction has been developed. Generalized scatter subtraction factors are introduced, and these factors are decomposed into terms dependent on the uniform (average) and spatially varying components of the source activity distribution. The variation of these factors with projection pixel location and gamma camera position is analysed for a simulated myocardial perfusion study with a 99Tc(m) source radionuclide and a non-uniform thorax model. Monte Carlo methods are used to model photon transport and detection. The application of pixel-dependent scatter subtraction factors for scatter compensation is evaluated in an image reconstruction experiment for this simulated myocardial perfusion study. Generalized matrix inverses with noise-dependent regularization are used for image reconstruction. For this simulation, use of a pixel-dependent scatter subtraction factor and a constant scatter subtraction factor are effective for scatter compensation. Activity estimates within the left ventricular myocardium for these two methods are practically the same as those obtained from image reconstructions where the detection of Compton-scattered photons is included in the system matrix.

Heart Ventricles↗
PubMed2005

ASIAN: a web server for inferring a regulatory network framework from gene expression profiles.

The standard workflow in gene expression profile analysis to identify gene function is the clustering by various metrics and techniques, and the following analyses, such as sequence analyses of upstream regions. A further challenging analysis is the inference of a gene regulatory network, and some computational methods have been intensively developed to deduce the gene regulatory network. Here, we describe our web server for inferring a framework of regulatory networks from a large number of gene expression profiles, based on graphical Gaussian modeling (GGM) in combination with hierarchical clustering (http://eureka.ims.u-tokyo.ac.jp/asian). GGM is based on a simple mathematical structure, which is the calculation of the inverse of the correlation coefficient matrix between variables, and therefore, our server can analyze a wide variety of data within a reasonable computational time. The server allows users to input the expression profiles, and it outputs the dendrogram of genes by several hierarchical clustering techniques, the cluster number estimated by a stopping rule for hierarchical clustering and the network between the clusters by GGM, with the respective graphical presentations. Thus, the ASIAN (Automatic System for Inferring A Network) web server provides an initial basis for inferring regulatory relationships, in that the clustering serves as the first step toward identifying the gene function.

Cluster Analysis↗
PubMed1995

Linguistic aspects of speech synthesis.

The conversion of text to speech is seen as an analysis of the input text to obtain a common underlying linguistic description, followed by a synthesis of the output speech waveform from this fundamental specification. Hence, the comprehensive linguistic structure serving as the substrate for an utterance must be discovered by analysis from the text. The pronunciation of individual words in unrestricted text is determined by morphological analysis or letter-to-sound conversion, followed by specification of the word-level stress contour. In addition, many text character strings, such as titles, numbers, and acronyms, are abbreviations for normal words, which must be derived. To further refine these pronunciations and to discover the prosodic structure of the utterance, word part of speech must be computed, followed by a phrase-level parsing. From this structure the prosodic structure of the utterance can be determined, which is needed in order to specify the durational framework and fundamental frequency contour of the utterance. In discourse contexts, several factors such as the specification of new and old information, contrast, and pronominal reference can be used to further modify the prosodic specification. When the prosodic correlates have been computed and the segmental sequence is assembled, a complete input suitable for speech synthesis has been determined. Lastly, multilingual systems utilizing rule frameworks are mentioned, and future directions are characterized.

Communication↗
PubMed2004

Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling.

Hybrid automata are an eminently suitable modelling framework for biological protein regulatory networks, as the protein concentration dynamics inside each biological cell are modelled using linear differential equations; inputs activate or deactivate these continuous dynamics through discrete switches, which themselves are controlled by protein concentrations reaching given thresholds. This paper proposes an iterative refinement algorithm for computing discrete abstractions of a class of hybrid automata with piecewise affine continuous dynamics and forced discrete transitions, defined completely in terms of symbolic variables and parameters. Furthermore, these discrete abstractions are utilised to compute symbolic parametric backward reachable sets from the equilibria of the hybrid automata, that are guaranteed to be exact or conservative under-approximations. The algorithm is then implemented using MATLAB and QEPCAD, to compute reachable sets for the biologically observed equilibria of the multiple cell Delta-Notch protein signalling automaton with symbolic parameters. The results are analysed to show that novel, non-intuitive, and biologically interesting properties can be deduced from the reachability computation, thus demonstrating the utility of the algorithm.

Algorithms↗
PubMed1999

Three-dimensional artifact induced by projection weighting and misalignment.

In recent years, the use of computer graphic techniques to produce three-dimensional (3-D) and reformatted images from a set of axial computed tomography (CT) images has gained significant interest. In most cases, the CT images are generated with the projection data set weighted prior to reconstruction, to combat motion artifacts, data inconsistency, or redundant data samples. In this paper, we investigate the potential bias introduced to the reconstruction as a result of the interaction of the projection weights and the isocenter misalignment (ISM). We demonstrate that when the weights applied to the conjugate rays are significantly different, bias will result which favors the sample with a higher weight. Although the error is not easily detected in axial CT images, it can be quite visible in 3-D or multiplanar reformatted (MPR) images. In this paper, we first present a theoretical framework to analyze and predict the bias. The theoretical prediction is validated by both computer simulations and phantom experiments. Several schemes to combat this artifact are subsequently presented; and their effectiveness is demonstrated.

Artifacts↗
PubMed2006

The measurement of congenital nasal pyriform aperture stenosis in infant.

OBJECTIVE: In the study we use the image of three dimensional computed tomography (3D-CT) to assess the different widths of the bony framework of congenital nasal pyriform aperture stenosis (CNPAS). METHODS: We select 17 infants under 4 months old diagnosed as CNPAS for this study. There were four categories of distance measurement. The distance between the caudal end of the nasal bone (nasal tip) and the anterior nasal spine (NPAH). The distance between bilateral bony inner wall of the nasal pyriform aperture at the midpoint of the aperture height (MIVD). The interprocess distance at the level of lower 1/4 of the pyriform aperture height (IPD). The narrowest distance between the bilateral nasal processes (NIPD). RESULTS: There were 17 infants, nine males and eight females. At the time of performing 3D-CT, the mean age was 49.5+/-35.9 days. The results of measurement were: NPAH: 10.9+/-1.23mm, MIVD: 8.2+/-0.89mm, IPD: 4.9+/-0.93mm, and NIPD: 4.4+/-0.73mm. The MIVD is significantly wider than both IPD and NIPD (p<0.01). There is high correlation between IPD and NIPD. There is no significant difference on age between gender in this study. However, the IPD (4.4+/-0.74) and NIPD (3.9+/-0.47) of male patients are broader, respectively, than those of female patients with significant difference (p<0.05). CONCLUSION: The measurement of CNPAS by means of 3D-CT may provide useful data for evaluation of the width in different parts of nasal pyriform aperture. These may be used for evaluation of pre- and postoperative status and future investigation in CNPAS patients.

Constriction, Pathologic↗
PubMed2004

An empirical Bayes approach to inferring large-scale gene association networks.

MOTIVATION: Genetic networks are often described statistically using graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis where the sample size is small compared to the number of considered genes. This renders many standard algorithms for graphical models inapplicable, and inferring genetic networks an 'ill-posed' inverse problem. METHODS: We introduce a novel framework for small-sample inference of graphical models from gene expression data. Specifically, we focus on the so-called graphical Gaussian models (GGMs) that are now frequently used to describe gene association networks and to detect conditionally dependent genes. Our new approach is based on (1) improved (regularized) small-sample point estimates of partial correlation, (2) an exact test of edge inclusion with adaptive estimation of the degree of freedom and (3) a heuristic network search based on false discovery rate multiple testing. Steps (2) and (3) correspond to an empirical Bayes estimate of the network topology. RESULTS: Using computer simulations, we investigate the sensitivity (power) and specificity (true negative rate) of the proposed framework to estimate GGMs from microarray data. This shows that it is possible to recover the true network topology with high accuracy even for small-sample datasets. Subsequently, we analyze gene expression data from a breast cancer tumor study and illustrate our approach by inferring a corresponding large-scale gene association network for 3883 genes.

Algorithms↗
PubMed2006

Computational methodologies for modelling, analysis and simulation of signalling networks.

This article is a critical review of computational techniques used to model, analyse and simulate signalling networks. We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication. In order to avoid an overly abstract and general discussion, we focus on three case studies in the areas of receptor signalling and kinase cascades, cell-cycle regulation and wound healing. We report on a variety of modelling techniques and associated tools, in addition to the traditional approach based on ordinary differential equations (ODEs), which provide a range of descriptive and analytical powers. As the field matures, we expect a wider uptake of these alternative approaches for several reasons, including the need to take into account low protein copy numbers and noise and the great complexity of cellular organisation. An advantage offered by many of these alternative techniques, which have their origins in computing science, is the ability to perform sophisticated model analysis which can better relate predicted behaviour and observations.

Algorithms↗
PubMed2003

Computational tools for modeling electrical activity in cardiac tissue.

Computer models offer many attractive benefits. However, the modeling of cardiac tissue is computationally expensive due to several physical constraints which result in fine spatiotemporal discretization over large spatiotemporal regions. Our laboratory has been actively trying to develop new techniques to make large scale cardiac simulations tractable over the past 15 years. This paper describes the latest modeling software that our group has developed, called Carp (Cardiac arrhythmias research package). It is designed to run in both shared memory and clustered computing environments. Carp aims to be modular and flexible by following a plug-in framework. This allows the latest models and most efficient solvers to be incorporated as well as enabling run-time selection of techniques. Performance results are given for a large-scale simulation which utilized a comprehensive membrane ionic current description.

Action Potentials↗
PubMed2006

Tomographic reconstruction using an adaptive tetrahedral mesh defined by a point cloud.

Medical images in nuclear medicine are commonly represented in three dimensions as a stack of two-dimensional images that are reconstructed from tomographic projections. Although natural and straightforward, this may not be an optimal visual representation for performing various diagnostic tasks. A method for three-dimensional (3-D) tomographic reconstruction is developed using a point cloud image representation. A point cloud is a set of points (nodes) in space, where each node of the point cloud is characterized by its position and intensity. The density of the nodes determines the local resolution allowing for the modeling of different parts of the image with different resolution. The reconstructed volume, which in general could be of any resolution, size, shape, and topology, is represented by a set of nonoverlapping tetrahedra defined by the nodes. The intensity at any point within the volume is defined by linearly interpolating inside a tetrahedron from the values at the four nodes that define the tetrahedron. This approach creates a continuous piecewise linear intensity over the reconstruction domain. The reconstruction provides a distinct multiresolution representation, which is designed to accurately and efficiently represent the 3-D image. The method is applicable to the acquisition of any tomographic geometry, such as parallel-, fan-, and cone-beam; and the reconstruction procedure can also model the physics of the image detection process. An efficient method for evaluating the system projection matrix is presented. The system matrix is used in an iterative algorithm to reconstruct both the intensity and location of the distribution of points in the point cloud. Examples of the reconstruction of projection data generated by computer simulations and projection data experimentally acquired using a Jaszczak cardiac torso phantom are presented. This work creates a framework for voxel-less multiresolution representation of images in nuclear medicine.

Algorithms↗
PubMed2004

The challenges of imaging based computational fluid dynamics.

Image based Computational Fluid Dynamics (CFD) simulation of the cardiovascular system is increasingly becoming important and its application in everyday medical practice can already be envisaged. The goal of this workshop is to address all the factors involved in the development of a computational framework/software for modelling and analyses of the cardiovascular system and provide examples. The development of such framework, requires integration, management and interpretation of data from several technology areas such as a) feature detection and extraction of arterial geometry from imaging data, b) adaptive grid generation techniques for 3-D asymmetric geometries c) hemodynamic modelling, disparate length-scale model, and fluid-tissue interaction with high-performance computing, d) CFD data validation, e) feature extraction/detection and visualisation algorithms, f) graphical user interface to allow remote visualisation of post processed data. These computational tools are employed to study flow in specific problem sites in the vascular tree such as the carotid, femoral, coronary and abdominal arteries. Such studies provide understanding of the factors involved in the initialisation and evolution of arterial disease due to altered flow conditions (as a result of plaque formation) such as flow separation and reversal, and low and oscillatory wall shear stress. It is also used to study the effect of various clinical procedures such as the implantation of stents, vascular grafts, vascular prostheses and artificial valve implants on local and global hemodynamics. This workshop will address a new emerging paradigm in clinical practice known as predictive medicine for effective surgical planning and post surgical rehabilitation. The workshop will also address the difficulties in the implementation of some of the technology areas in this application with examples of carotid, femoral, and abdominal artery simulations.

Algorithms↗
PubMed1989

Improving toxicology testing protocols using computer simulations.

Computer simulation can be used to integrate existing toxicity information within a biologically realistic framework. Simulation models calculate relevant measures of target tissue dose based on physiological, biochemical and physicochemical properties and readily support the dose, route, species and interchemical extrapolations necessary for human risk assessment. Because these models require very specific information, much of which can be obtained in vitro, they are much less dependent on extensive animal experiments than conventional risk assessment methods. With continuing development, simulation modeling will become an invaluable tool for improving experimental designs, for interpreting animal toxicity tests, and for estimating the importance of the animal toxicity observations for people.

Administration, Inhalation↗
PubMed2000

Analysis of the direct Fourier method for computer tomography.

We develop a direct Fourier method (DFM) for reconstructing a function from its X-ray projections. We introduce a framework that can be used to get a quantitative comparison between different choices of basis functions in the step of resampling from polar to Cartesian coordinates. We use the framework to compare polynomial interpolation, approximated sinc-functions, Gaussians, splines, and Kaiser-Bessel functions. The resulting algorithm is very fast, requiring 12.5N2 log2 N + 49N2 flops. Numerical experiments show it to be efficient.

Algorithms↗
PubMed2002

Data Grids: a new computational infrastructure for data-intensive science.

Twenty-first-century scientific and engineering enterprises are increasingly characterized by their geographic dispersion and their reliance on large data archives. These characteristics bring with them unique challenges. First, the increasing size and complexity of modern data collections require significant investments in information technologies to store, retrieve and analyse them. Second, the increased distribution of people and resources in these projects has made resource sharing and collaboration across significant geographic and organizational boundaries critical to their success. In this paper I explore how computing infrastructures based on Data Grids offer data-intensive enterprises a comprehensive, scalable framework for collaboration and resource sharing. A detailed example of a Data Grid framework is presented for a Large Hadron Collider experiment, where a hierarchical set of laboratory and university resources comprising petaflops of processing power and a multi-petabyte data archive must be efficiently used by a global collaboration. The experience gained with these new information systems, providing transparent managed access to massive distributed data collections, will be applicable to large-scale, data-intensive problems in a wide spectrum of scientific and engineering disciplines, and eventually in industry and commerce. Such systems will be needed in the coming decades as a central element of our information-based society.

Computer Communication Networks↗